Buggy code:
Component glassPane ; GhostGlassPane dNdGlassPane ; public static Cursor fistCursor ; public static Cursor zoomInCursor ; public static Cursor zoomOutCursor ; public static Cursor dragNDropCursor ; Session session ; private GenomeManager genomeManager ; private String groupByAttribute = null ; private Map < String , List < Track > > overlayTracksMap = new HashMap ( ) ; private Set < Track > overlaidTracks = new HashSet ( ) ; public static final String DATA_PANEL_NAME = "DataPanel" ; public static final String FEATURE_PANEL_NAME = "FeaturePanel" ; private LinkedList < String > recentSessionList = new LinkedList < String > ( ) ; private boolean isExportingSnapshot = false ; Collection < SoftReference < TrackGroupEventListener > > groupListeners = Collections . synchronizedCollection ( new ArrayList < SoftReference < TrackGroupEventListener > > ( ) ) ; Collection < SoftReference < AlignmentTrackEventListener > > alignmentTrackListeners = Collections . synchronizedCollection ( new ArrayList < SoftReference < AlignmentTrackEventListener > > ( ) ) ; private List < JComponent > otherToolMenus = new ArrayList < JComponent > ( ) ; private boolean rulerEnabled ; public void addOtherToolMenu ( JComponent menu ) { } List < JComponent > getOtherToolMenus ( ) { } @ Subscribe public void receiveViewChange ( ViewChange . Result e ) { } @ Subscribe public void receiveViewChange ( ViewChange . ChromosomeChangeResult e ) { } public static IGV createInstance ( Frame frame ) { } public static IGV getInstance ( ) { } @ ForTesting static void destroyInstance ( ) { } public static boolean hasInstance ( ) { } public static JRootPane getRootPane ( ) { } public static Frame getMainFrame ( ) { } private IGV ( Frame frame ) { } public void repaint ( ) { } public GhostGlassPane getDnDGlassPane ( ) { } public void startDnD ( ) { } public void endDnD ( ) { } public Dimension getPreferredSize ( ) { } public void addRegionOfInterest ( RegionOfInterest roi ) { } void beginROI ( JButton button ) { } public void endROI ( ) { } private void chromosomeChangeEvent ( String chrName , boolean updateCommandBar ) { } public void repaintStatusAndZoomSlider ( ) { } public static void repaintPanelsHeadlessSafe ( ) { } public void repaintDataAndHeaderPanels ( ) { } public void repaintDataPanels ( ) { } public void repaintDataAndHeaderPanels ( boolean updateCommandBar ) { } public void repaintNamePanels ( ) { } public void selectGenomeFromList ( String genomeId ) { } public Collection < String > getSelectableGenomeIDs ( ) { } public void doDefineGenome ( ProgressMonitor monitor ) { } public GenomeListItem getGenomeSelectedInDropdown ( ) { } public Collection < String > getGenomeDisplayNames ( ) { } void loadGenomeFromServerAction ( ) { } public void doLoadGenome ( ProgressMonitor monitor ) { } public void loadGenomeById ( String genomeId ) { } public void loadGenome ( String path , ProgressMonitor monitor , boolean userDefined ) throws IOException { } public void loadGenome ( String path , ProgressMonitor monitor , boolean addGenomeTrack , boolean userDefined ) throws IOException { File file = new File ( path ) ; if ( file . exists ( ) ) { File directory = file . getAbsoluteFile ( ) . getParentFile ( ) ; PreferenceManager . getInstance ( ) . setLastGenomeImportDirectory ( directory ) ; } resetSession ( null ) ; Genome genome = getGenomeManager ( ) . loadGenome ( path , monitor , addGenomeTrack ) ; if ( genome == null ) return ; final String name = genome . getDisplayName ( ) ; final String id = genome . getId ( ) ; GenomeListItem genomeListItem = new GenomeListItem ( name , path , id ) ; getGenomeManager ( ) . addGenomeItem ( genomeListItem , userDefined ) ; IGVCommandBar cmdBar = contentPane . getCommandBar ( ) ; cmdBar . refreshGenomeListComboBox ( ) ; cmdBar . selectGenome ( genomeListItem . getId ( ) ) ; cmdBar . updateChromosFromGenome ( genome ) ; <START_BUG> FrameManager . getDefaultFrame ( ) . setChromosomeName ( CHR_ALL , true ) ; <END_BUG> menuBar . createFileMenu ( ) ; } public void enableExtrasMenu ( ) { } public Future loadTracks ( final Collection < ResourceLocator > locators ) { } public List < Map < TrackPanelScrollPane , Integer > > getTrackPanelAttrs ( ) { } public void resetPanelHeights ( Map < TrackPanelScrollPane , Integer > trackCountMap , Map < TrackPanelScrollPane , Integer > panelSizeMap ) { } public void setGeneList ( GeneList geneList ) { } public void setGeneList ( final GeneList geneList , final boolean recordHistory ) { } public void setDefaultFrame ( String searchString ) { } public void resetFrames ( ) { } public final void doViewPreferences ( ) { } public final void doViewPreferences ( final String tabToSelect ) { } public final void saveStateForExit ( ) { } public final void doShowAttributeDisplay ( boolean enableAttributeView ) { } public final void doRefresh ( ) { } public final void refreshCommandBar ( ) { } public final void doSelectDisplayableAttribute ( ) { } public final void saveImage ( Component target ) { } public final void saveImage ( Component target , String title ) { } public boolean isExportingSnapshot ( ) { } public final void createSnapshot ( final Component target , final File defaultFile ) { } public String createSnapshotNonInteractive ( Component target , File file , boolean paintOffscreen ) throws IOException { } public File selectSnapshotFile ( File defaultFile ) { } private void createZoomCursors ( ) throws HeadlessException , IndexOutOfBoundsException { } private void createHandCursor ( ) throws HeadlessException , IndexOutOfBoundsException { } private void createDragAndDropCursor ( ) throws HeadlessException , IndexOutOfBoundsException { } public void resetSession ( String sessionPath ) { } public void newSession ( ) { } public void setStatusBarMessage ( String message ) { } public void setStatusBarPosition ( String message ) { } public void resetToFactorySettings ( ) { } public void setFilterMatchAll ( boolean value ) { } public boolean isFilterMatchAll ( ) { } public void setFilterShowAllTracks ( boolean value ) { }

Fix:
FrameManager . getDefaultFrame ( ) . setChromosomeName ( genome . getHomeChromosome ( ) , true ) ;